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When simple sequence comparison fails: the cryptic case of the shared domains of the bacterial replication initiation proteins DnaB and DnaD

Author(s)
Marston, Farhat Y.; Grainger, William H.; Smits, Wiep Klaas; Hopcroft, Nicholas H.; Green, Matthew; Hounslow, Andrea M.; Grossman, Alan D.; Craven, C. Jeremy; Soultanas, Panos; ... Show more Show less
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Abstract
DnaD and DnaB are essential DNA-replication-initiation proteins in low-G+C content Gram-positive bacteria. Here we use sensitive Hidden Markov Model-based techniques to show that the DnaB and DnaD proteins share a common structure that is evident across all their structural domains, termed DDBH1 and DDBH2 (DnaD DnaB Homology 1 and 2). Despite strong sequence divergence, many of the DNA-binding and oligomerization properties of these domains have been conserved. Although eluding simple sequence comparisons, the DDBH2 domains share the only strong sequence motif; an extremely highly conserved YxxxIxxxW sequence that contributes to DNA binding. Sequence alignments of DnaD alone fail to identify another key part of the DNA-binding module, since it includes a poorly conserved sequence, a solvent-exposed and somewhat unstable helix and a mobile segment. We show by NMR, in vitro mutagenesis and in vivo complementation experiments that the DNA-binding module of Bacillus subtilis DnaD comprises the YxxxIxxxW motif, the unstable helix and a portion of the mobile region, the latter two being essential for viability. These structural insights lead us to a re-evaluation of the oligomerization and DNA-binding properties of the DnaD and DnaB proteins.
Date issued
2010-05
URI
http://hdl.handle.net/1721.1/72957
Department
Massachusetts Institute of Technology. Department of Biology
Journal
Nucleic Acids Research
Publisher
Oxford University Press
Citation
Marston, F. Y. et al. “When Simple Sequence Comparison Fails: The Cryptic Case of the Shared Domains of the Bacterial Replication Initiation Proteins DnaB and DnaD.” Nucleic Acids Research 38.20 (2010): 6930–6942. Web.
Version: Final published version
ISSN
0305-1048
1362-4962

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